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Volumn 17, Issue 2, 2011, Pages 383-389

Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

(7) Ohno, Kazuki a Mitsui, Takashi b Tanida, Yoshiaki b Matsuura, Azuma b Fujitani, Hideaki b Niimi, Tatsuya a Orita, Masaya a

a ASTELLAS PHARMA INC (Japan)

b FUJITSU LABORATORIES LTD (Japan)

Author keywords

Binding free energy calculation; MM PBSA; MP CAFEE; Poly (ADP ribose) polymerase inhibitors

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE INHIBITOR;

ARTICLE; BINDING AFFINITY; ENERGY; EQUILIBRIUM CONSTANT; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR MECHANICS; NONHUMAN; POISSON DISTRIBUTION; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; SURFACE PROPERTY;

BINDING SITES; COMPUTER SIMULATION; DRUG DISCOVERY; ENZYME INHIBITORS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; POLY(ADP-RIBOSE) POLYMERASES; PROTEIN BINDING; THERMODYNAMICS;

EID: 79551582236 PISSN: 16102940 EISSN: 09485023 Source Type: Journal
DOI: 10.1007/s00894-010-0728-2 Document Type: Article

Times cited : (8)

References (36)

1
- 0142241246
- 1:CAS:528:DC%2BD3sXos1Sgurw%3D 10.1124/mol.64.5.1007
- PA Nguewa MA Fuertes C Alonso JM Petéz 2003 Mol Pharmacol 64 1007 1014 1:CAS:528:DC%2BD3sXos1Sgurw%3D 10.1124/mol.64.5.1007
- (2003) Mol Pharmacol , vol.64 , pp. 1007-1014
- Nguewa, P.A.¹ Fuertes, M.A.² Alonso, C.³ Petéz, J.M.⁴

2
- 0035063766
- 1:STN:280:DC%2BD3MrgsFaqsQ%3D%3D 10.1089/089771501750170912
- MC LaPlaca J Zhang R Raghupathi JH Li F Smith FM Bareyre SH Snyder DI Graham TK Mclntosh 2001 J Neurotrauma 18 369 376 1:STN:280: DC%2BD3MrgsFaqsQ%3D%3D 10.1089/089771501750170912
- (2001) J Neurotrauma , vol.18 , pp. 369-376
- Laplaca, M.C.¹ Zhang, J.² Raghupathi, R.³ Li, J.H.⁴ Smith, F.⁵ Bareyre, F.M.⁶ Snyder, S.H.⁷ Graham, D.I.⁸ McLntosh, T.K.⁹

3
- 0033545925
- 1:CAS:528:DyaK1MXjtFCnur0%3D 10.1073/pnas.96.10.5774
- AS Mandir S Przedborski V Jackson-Lewis Z Wang CM Simbulan-Rosenthal ME Smulson BE Hoffman DB Guastella VL Dawson TM Dawson 1999 Proc Natl Acad Sci USA 96 5774 5779 1:CAS:528:DyaK1MXjtFCnur0%3D 10.1073/pnas.96.10.5774
- (1999) Proc Natl Acad Sci USA , vol.96 , pp. 5774-5779
- Mandir, A.S.¹ Przedborski, S.² Jackson-Lewis, V.³ Wang, Z.⁴ Simbulan-Rosenthal, C.M.⁵ Smulson, M.E.⁶ Hoffman, B.E.⁷ Guastella, D.B.⁸ Dawson, V.L.⁹ Dawson, T.M.¹⁰

4
- 54549103449
- 1:CAS:528:DC%2BD1cXhtFeqs7vE 10.1021/jm8001263
- KA Menear C Adcock R Boulter XL Cockcroft CL Cranston A Dillon KJ J Drzewiecki S Garman S Gomez H Javaid F Kerrigan C Knights A Lau VM Loh Jr IT Matthews S Moore MJ O'Connor GC Smith NM Martin 2008 J Med Chem 51 6581 6591 1:CAS:528:DC%2BD1cXhtFeqs7vE 10.1021/jm8001263
- (2008) J Med Chem , vol.51 , pp. 6581-6591
- Menear, K.A.¹ Adcock, C.² Boulter, R.³ Cockcroft, X.L.⁴ Cranston, C.L.⁵ Dillon, K.J.A.⁶ Drzewiecki, J.⁷ Garman, S.⁸ Gomez, S.⁹ Javaid, H.¹⁰ Kerrigan, F.¹¹ Knights, C.¹² Lau, A.¹³ Loh Jr., V.M.¹⁴ Matthews, I.T.¹⁵ Moore, S.¹⁶ O'Connor, M.J.¹⁷ Smith, G.C.¹⁸ Martin, N.M.¹⁹

5
- 0037239590
- 1:CAS:528:DC%2BD3sXlt1GhsQ%3D%3D
- GJ Southan C Szabó 2003 Curr Med Chem 10 321 340 1:CAS:528:DC%2BD3sXlt1GhsQ%3D%3D
- (2003) Curr Med Chem , vol.10 , pp. 321-340
- Southan, G.J.¹ Szabó, C.²

6
- 69449086187
- 1:CAS:528:DC%2BD1MXot1aksLs%3D 10.2174/138920309788452209
- H Meirovitch S Cheluvaraja RP White 2009 Curr Protein Pept Sci 10 229 243 1:CAS:528:DC%2BD1MXot1aksLs%3D 10.2174/138920309788452209
- (2009) Curr Protein Pept Sci , vol.10 , pp. 229-243
- Meirovitch, H.¹ Cheluvaraja, S.² White, R.P.³

7
- 69549138254
- 1:CAS:528:DC%2BD1MXptFChsrs%3D 10.1021/ci9002156
- Y Fukunishi D Mitomo H Nakamura 2009 J Chem Inf Model 49 1944 1951 1:CAS:528:DC%2BD1MXptFChsrs%3D 10.1021/ci9002156
- (2009) J Chem Inf Model , vol.49 , pp. 1944-1951
- Fukunishi, Y.¹ Mitomo, D.² Nakamura, H.³

8
- 20844437061
- 1:CAS:528:DC%2BD2MXhtVGnu70%3D 10.1038/nbt1059
- GL Card L Blasdel BP England C Zhang Y Suzuki S Gillette D Fong PN Ibrahim DR Artis G Bollag MV Milburn SH Kim J Schlessinger KY Zhang 2005 Nat Biotechnol 23 201 207 1:CAS:528:DC%2BD2MXhtVGnu70%3D 10.1038/nbt1059
- (2005) Nat Biotechnol , vol.23 , pp. 201-207
- Card, G.L.¹ Blasdel, L.² England, B.P.³ Zhang, C.⁴ Suzuki, Y.⁵ Gillette, S.⁶ Fong, D.⁷ Ibrahim, P.N.⁸ Artis, D.R.⁹ Bollag, G.¹⁰ Milburn, M.V.¹¹ Kim, S.H.¹² Schlessinger, J.¹³ Zhang, K.Y.¹⁴

9
- 33746872935
- 1:CAS:528:DC%2BD28XmvFGjs7s%3D 10.1021/jm060522a
- PD Lyne ML Lamb JC Saeh 2006 J Med Chem 49 4805 4808 1:CAS:528: DC%2BD28XmvFGjs7s%3D 10.1021/jm060522a
- (2006) J Med Chem , vol.49 , pp. 4805-4808
- Lyne, P.D.¹ Lamb, M.L.² Saeh, J.C.³

10
- 40949163431
- 1:CAS:528:DC%2BD1cXhvFWgurk%3D 10.1021/ja0771033
- R Abel T Young R Farid BJ Berne RA Friesner 2008 J Am Chem Soc 130 2817 2831 1:CAS:528:DC%2BD1cXhvFWgurk%3D 10.1021/ja0771033
- (2008) J Am Chem Soc , vol.130 , pp. 2817-2831
- Abel, R.¹ Young, T.² Farid, R.³ Berne, B.J.⁴ Friesner, R.A.⁵

11
- 0024578173
- 1:CAS:528:DyaL1MXlvVajsLs%3D 10.1146/annurev.bb.18.060189.002243
- DL Beveridge FM DiCapua DL Beveridge FM DiCapua 1989 Annu Rev Biophys Biophys Chem 18 431 492 1:CAS:528:DyaL1MXlvVajsLs%3D 10.1146/annurev.bb.18. 060189.002243
- (1989) Annu Rev Biophys Biophys Chem , vol.18 , pp. 431-492
- Beveridge, D.L.¹ Dicapua, F.M.² Beveridge, D.L.³ Dicapua, F.M.⁴

12
- 7044239742
- 1:CAS:528:DyaK3sXmt1Sktr0%3D 10.1021/cr00023a004
- P Kollman 1993 Chem Rev 93 2395 2417 1:CAS:528:DyaK3sXmt1Sktr0%3D 10.1021/cr00023a004
- (1993) Chem Rev , vol.93 , pp. 2395-2417
- Kollman, P.¹

13
- 4243754128
- 1:CAS:528:DyaK2sXisVSrt7c%3D 10.1103/PhysRevLett.78.2690
- C Jarzynski 1997 Phys Rev Lett 78 2690 2693 1:CAS:528:DyaK2sXisVSrt7c%3D 10.1103/PhysRevLett.78.2690
- (1997) Phys Rev Lett , vol.78 , pp. 2690-2693
- Jarzynski, C.¹

14
- 0242677537
- 10.1103/PhysRevLett.91.140601
- MR Shirts E Bair G Hooker VS Pande 2003 Phys Rev Lett 91 140601 10.1103/PhysRevLett.91.140601
- (2003) Phys Rev Lett , vol.91 , pp. 140601
- Shirts, M.R.¹ Bair, E.² Hooker, G.³ Pande, V.S.⁴

15
- 63149192208
- 10.1103/PhysRevE.79.021914
- H Fujitani Y Tanida A Matsuura 2009 Phys Rev E 79 021914 10.1103/PhysRevE.79.021914
- (2009) Phys Rev e , vol.79 , pp. 021914
- Fujitani, H.¹ Tanida, Y.² Matsuura, A.³

16
- 34547830982
- 1:CAS:528:DC%2BD2sXpt1Shtrw%3D 10.1016/j.chemphys.2007.07.014
- Y Tanida M Ito H Fujitani 2007 Chem Phys 337 135 143 1:CAS:528: DC%2BD2sXpt1Shtrw%3D 10.1016/j.chemphys.2007.07.014
- (2007) Chem Phys , vol.337 , pp. 135-143
- Tanida, Y.¹ Ito, M.² Fujitani, H.³

17
- 3843071128
- 1:CAS:528:DC%2BD2cXls1Kqtr4%3D 10.1021/jm0499256
- K Hattori Y Kido H Yamamoto J Ishida K Kamijo K Murano M Ohkubo T Kinoshita A Iwashita K Mihara S Yamazaki N Matsuoka Y Teramura H Miyake 2004 J Med Chem 47 4151 4154 1:CAS:528:DC%2BD2cXls1Kqtr4%3D 10.1021/jm0499256
- (2004) J Med Chem , vol.47 , pp. 4151-4154
- Hattori, K.¹ Kido, Y.² Yamamoto, H.³ Ishida, J.⁴ Kamijo, K.⁵ Murano, K.⁶ Ohkubo, M.⁷ Kinoshita, T.⁸ Iwashita, A.⁹ Mihara, K.¹⁰ Yamazaki, S.¹¹ Matsuoka, N.¹² Teramura, Y.¹³ Miyake, H.¹⁴

18
- 0346725042
- 1:CAS:528:DC%2BD2cXoslOh 10.1016/S0014-5793(03)01362-0
- T Kinoshita I Nakanishi M Warizuka Y Iwashita Y Kido K Hattori T Fujii 2004 FEBS Lett 556 43 46 1:CAS:528:DC%2BD2cXoslOh 10.1016/S0014-5793(03)01362-0
- (2004) FEBS Lett , vol.556 , pp. 43-46
- Kinoshita, T.¹ Nakanishi, I.² Warizuka, M.³ Iwashita, Y.⁴ Kido, Y.⁵ Hattori, K.⁶ Fujii, T.⁷

19
- 79551574620
- MOE is a product of Chemical Computing Group, Inc, 1010 Sherbrooke Street West, Suite 910, Montreal, Quebec, Canada
- MOE is a product of Chemical Computing Group, Inc, 1010 Sherbrooke Street West, Suite 910, Montreal, Quebec, Canada

20
- 79551609405
- Gold is a product of a collaboration between the University of Sheffield, GlaxoSmithKline plc and Cambridge Structural Database System (CCDC). It is available from CCDC (12 Union Road, Cambridge, CB2 1EZ, UK)
- Gold is a product of a collaboration between the University of Sheffield, GlaxoSmithKline plc and Cambridge Structural Database System (CCDC). It is available from CCDC (12 Union Road, Cambridge, CB2 1EZ, UK)

21
- 0029633168
- 1:CAS:528:DyaK2MXps1Wrtr0%3D 10.1016/0010-4655(95)00042-E
- HJC Berendsen D van der Spoel R van Drunen 1995 Comput Phys Commun 91 43 46 1:CAS:528:DyaK2MXps1Wrtr0%3D 10.1016/0010-4655(95)00042-E
- (1995) Comput Phys Commun , vol.91 , pp. 43-46
- Berendsen, H.J.C.¹ Van Der Spoel, D.² Van Drunen, R.³

22
- 0035789518
- 1:CAS:528:DC%2BD3MXnsVGjsL4%3D
- E Lindahl B Hess D van der Spoel 2001 J Mol Model 7 306 317 1:CAS:528:DC%2BD3MXnsVGjsL4%3D
- (2001) J Mol Model , vol.7 , pp. 306-317
- Lindahl, E.¹ Hess, B.² Van Der Spoel, D.³

23
- 27344454932
- 10.1002/jcc.20291
- D van der Spoel E Lindahl B Hess G Groenhof AE Mark HJC Berendsen 2005 J Comput Chem 26 1701 1718 10.1002/jcc.20291
- (2005) J Comput Chem , vol.26 , pp. 1701-1718
- Van Der Spoel, D.¹ Lindahl, E.² Hess, B.³ Groenhof, G.⁴ Mark, A.E.⁵ Berendsen, H.J.C.⁶

24
- 84893169025
- 1:CAS:528:DyaK2cXhsFaqtQ%3D%3D 10.1002/jcc.540141112
- MW Schmidt KK Baldridge JA Boatz ST Elbert MS Gordon JH Jensen S Koseki N Matsunaga KA Nguyen S Su TL Windus M Dupuis JA Montgomery 1993 J Comput Chem 14 1347 1363 1:CAS:528:DyaK2cXhsFaqtQ%3D%3D 10.1002/jcc.540141112
- (1993) J Comput Chem , vol.14 , pp. 1347-1363
- Schmidt, M.W.¹ Baldridge, K.K.² Boatz, J.A.³ Elbert, S.T.⁴ Gordon, M.S.⁵ Jensen, J.H.⁶ Koseki, S.⁷ Matsunaga, N.⁸ Nguyen, K.A.⁹ Su, S.¹⁰ Windus, T.L.¹¹ Dupuis, M.¹² Montgomery, J.A.¹³

25
- 85127021441
- Elsevier Amsterdam
- Gordon MS, Schmidt MW (2005) Theory and Applications of Computational Chemistry: the first forty years. Elsevier, Amsterdam
- (2005) Theory and Applications of Computational Chemistry: The First Forty Years
- Gordon, M.S.¹ Schmidt, M.W.²

26
- 3042524904
- 1:CAS:528:DyaK3sXlvVyqsLs%3D 10.1021/j100142a004
- CI Bayly P Cieplak W Cornell PA Kollman 1993 J Phys Chem 97 10269 10280 1:CAS:528:DyaK3sXlvVyqsLs%3D 10.1021/j100142a004
- (1993) J Phys Chem , vol.97 , pp. 10269-10280
- Bayly, C.I.¹ Cieplak, P.² Cornell, W.³ Kollman, P.A.⁴

27
- 33748538349
- 10.1016/j.jmgm.2005.12.005
- J Wang W Wang PA Kollman DA Case 2006 J Mol Graph Model 25 247 260 10.1016/j.jmgm.2005.12.005
- (2006) J Mol Graph Model , vol.25 , pp. 247-260
- Wang, J.¹ Wang, W.² Kollman, P.A.³ Case, D.A.⁴

28
- 2942532422
- 1:CAS:528:DC%2BD2cXksFakurc%3D 10.1002/jcc.20035
- J Wang RM Wolf JW Caldwell PA Kollman DA Case 2004 J Comput Chem 25 1157 1174 1:CAS:528:DC%2BD2cXksFakurc%3D 10.1002/jcc.20035
- (2004) J Comput Chem , vol.25 , pp. 1157-1174
- Wang, J.¹ Wolf, R.M.² Caldwell, J.W.³ Kollman, P.A.⁴ Case, D.A.⁵

29
- 65249106601
- 1:CAS:528:DC%2BD1MXjsFyku7w%3D 10.1021/ct8005437
- H Fujitani A Matsuura S Sakai H Sato Y Tanida 2009 J Chem Theor Comput 5 1155 1156 1:CAS:528:DC%2BD1MXjsFyku7w%3D 10.1021/ct8005437
- (2009) J Chem Theor Comput , vol.5 , pp. 1155-1156
- Fujitani, H.¹ Matsuura, A.² Sakai, S.³ Sato, H.⁴ Tanida, Y.⁵

30
- 0004016501
- 1:CAS:528:DyaL3sXksF2htL4%3D 10.1063/1.445869
- WL Jorgensen J Chandrasekhar JD Madura RW Impey ML Klein 1983 J Chem Phys 79 926 935 1:CAS:528:DyaL3sXksF2htL4%3D 10.1063/1.445869
- (1983) J Chem Phys , vol.79 , pp. 926-935
- Jorgensen, W.L.¹ Chandrasekhar, J.² Madura, J.D.³ Impey, R.W.⁴ Klein, M.L.⁵

31
- 84943502952
- 10.1080/00268978400101201
- S Nosé 1984 Mol Phys 52 255 268 10.1080/00268978400101201
- (1984) Mol Phys , vol.52 , pp. 255-268
- Nosé, S.¹

32
- 0001538909
- 10.1103/PhysRevA.31.1695
- WG Hoover 1985 Phys Rev A 31 1695 1697 10.1103/PhysRevA.31.1695
- (1985) Phys Rev A , vol.31 , pp. 1695-1697
- Hoover, W.G.¹

33
- 33750587438
- Molecular dynamics with coupling to an external bath
- 1:CAS:528:DyaL2cXmtlGksbY%3D 10.1063/1.448118
- HJC Berendsen JPM Postma WF van Gunsteren A DiNola JR Haak 1984 Molecular dynamics with coupling to an external bath J Chem Phys 81 3684 3690 1:CAS:528:DyaL2cXmtlGksbY%3D 10.1063/1.448118
- (1984) J Chem Phys , vol.81 , pp. 3684-3690
- Berendsen, H.J.C.¹ Postma, J.P.M.² Van Gunsteren, W.F.³ Dinola, A.⁴ Haak, J.R.⁵

34
- 0000388705
- 1:CAS:528:DyaK2sXlvV2nu7g%3D 10.1002/(SICI)1096-987X(199709)18: 12<1463::AID-JCC4>3.0.CO;2-H
- B Hess H Bekker HJC Berendsen JGEM Fraaije 1997 J Comput Chem 18 1463 1472 1:CAS:528:DyaK2sXlvV2nu7g%3D 10.1002/(SICI)1096-987X(199709)18:12<1463:: AID-JCC4>3.0.CO;2-H
- (1997) J Comput Chem , vol.18 , pp. 1463-1472
- Hess, B.¹ Bekker, H.² Berendsen, H.J.C.³ Jgem, F.⁴

35
- 34247186195
- University of California San Francisco
- Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9. University of California, San Francisco
- (2006) AMBER 9
- Case, D.A.¹ Darden, T.A.² Cheatham Iii, T.E.³ Simmerling, C.L.⁴ Wang, J.⁵ Duke, R.E.⁶ Luo, R.⁷ Merz, K.M.⁸ Pearlman, D.A.⁹ Crowley, M.¹⁰ Walker, R.C.¹¹ Zhang, W.¹² Wang, B.¹³ Hayik, S.¹⁴ Roitberg, A.¹⁵ Seabra, G.¹⁶ Wong, K.F.¹⁷ Paesani, F.¹⁸ Wu, X.¹⁹ Brozell, S.²⁰ more..

36
- 25844492293
- 1:CAS:528:DC%2BD2MXns1aiur0%3D 10.1021/ct0500904
- C Chang W Chen MK Gilson 2005 J Chem Theor Comput 1 1017 1028 1:CAS:528:DC%2BD2MXns1aiur0%3D 10.1021/ct0500904
- (2005) J Chem Theor Comput , vol.1 , pp. 1017-1028
- Chang, C.¹ Chen, W.² Gilson, M.K.³

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